Insights into docking and scoring neuronal α4β2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations

A combined quantum mechanical (QM)‐polarized docking and molecular dynamics approach to study the binding mode and to predict the binding affinity of ligands acting at the α4β2‐nAChR is presented. The results obtained in this study indicate that the quantum mechanical/molecular mechanics docking protocol well describes the charge‐driven interactions occurring in the binding of nicotinic agonists, and it is able to represent the polarization effects on the ligand exerted by the surrounding atoms of the receptor at the binding site. This makes it possible to properly score agonists of α4β2‐nAChR and to reproduce the experimental binding affinity data with good accuracy, within a mean error of 2.2 kcal/mol. Moreover, applying the QM‐polarized docking to an ensemble of nAChR conformations obtained from MD simulations enabled us to accurately capture nAChR‐ligand induced‐fit effects. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Synthesis and evaluation of stereopure α-trifluoromethyl-malic hydroxamates as inhibitors of matrix metalloproteinases

The total synthesis of trifluoromethyl (Tfm) analogs of known nanomolar matrix metalloproteinases (MMPs) inhibitors has been performed. The synthetic protocol is based on a moderately stereoselective aldol reaction of trifluoropyruvate with an N-acyl-oxazolidin-2-thione for the construction of the core α-Tfm-malic unit. Both the diastereomeric forms of the target α-Tfm-malic hydroxamates showed micromolar inhibitory potency toward MMP-2 and 9, with a substantial drop with respect to the parent unfluorinated compounds.     

Discrete negative refraction in photonic crystal waveguide arrays

We report a systematic analysis of anomalous refractive effects at interfaces between two photonic crystal waveguide arrays. Discrete negative refraction can be easily predicted from the sign of the coupling coefficient between adjacent waveguides, regardless of handedness of propagation.     

Local branching

The availability of effective exact or heuristic solution methods for general Mixed-Integer Programs (MIPs) is of paramount importance for practical applications. In the present paper we investigate the use of a generic MIP solver as a black-box ``tactical' tool to explore effectively suitable solution subspaces defined and controlled at a ``strategic' level by a simple external branching framework. The procedure is in the spirit of well-known local search metaheuristics, but the neighborhoods are obtained through the introduction in the MIP model of completely general linear inequalities called local branching cuts. The new solution strategy is exact in nature, though it is designed to improve the heuristic behavior of the MIP solver at hand. It alternates high-level strategic branchings to define the solution neighborhoods, and low-level tactical branchings to explore them. The result is a completely general scheme aimed at favoring early updatings of the incumbent solution, hence producing high-quality solutions at early stages of the computation. The method is analyzed computationally on a large class of very difficult MIP problems by using the state-of-the-art commercial software ILOG-Cplex 7.0 as the black-box tactical MIP solver. For these instances, most of which cannot be solved to proven optimality in a reasonable time, the new method exhibits consistently an improved heuristic performance: in 23 out of 29 cases, the MIP solver produced significantly better incumbent solutions when driven by the local branching paradigm. Mathematics Subject Classification (2000):90C06, 90C10, 90C11, 90C27, 90C59     

Current status of the TwinMic beamline at Elettra: a soft X‐ray transmission and emission microscopy station

The current status of the TwinMic beamline at Elettra synchrotron light source, that hosts the European twin X‐ray microscopy station, is reported. The X‐ray source, provided by a short hybrid undulator with source size and divergence intermediate between bending magnets and conventional undulators, is energy‐tailored using a collimated plane‐grating monochromator. The TwinMic spectromicroscopy experimental station combines scanning and full‐field imaging in a single instrument, with contrast modes such as absorption, differential phase, interference and darkfield. The implementation of coherent diffractive imaging modalities and ptychography is ongoing. Typically, scanning transmission X‐ray microscopy images are simultaneously collected in transmission and differential phase contrast and can be complemented by chemical and elemental analysis using across‐absorption‐edge imaging, X‐ray absorption near‐edge structure or low‐energy X‐ray fluorescence. The lateral resolutions depend on the particular imaging and contrast mode chosen. The TwinMic range of applications covers diverse research fields such as biology, biochemistry, medicine, pharmacology, environment, geochemistry, food, agriculture and materials science. They will be illustrated in the paper with representative results.     

Constraining extended theories of gravity using Solar System tests

Solar System tests give nowadays constraints on the estimated value of the cosmological constant, which can be accurately derived from different experiments regarding gravitational redshift, light deflection, gravitational time-delay and geodesic precession. Assuming that each reasonable theory of gravitation should satisfy Solar System tests, we use these limits on the estimated value of the cosmological constant to constrain extended theories of Gravity, which are nowadays studied as possible theories for cosmological models and provide viable solutions to the cosmological constant problem and the explanation of the present acceleration of the Universe. We obtain that the estimated values, from Solar System tests, for the parameters appearing in the extended theories of Gravity are orders of magnitude bigger than the values obtained in the framework of cosmologically relevant theories.     

Topological Polymer Chemistry Enters Surface Science: Linear versus Cyclic Polymer Brushes

The cyclic polymer topology strongly alters the interfacial, physico‐chemical properties of polymer brushes, when compared to the linear counterparts. In this study, we especially concentrated on poly‐2‐ethyl‐2‐oxazoline (PEOXA) cyclic and linear grafts assembled on titanium oxide surfaces by the “grafting‐to” technique. The smaller hydrodynamic radius of ring PEOXAs favors the formation of denser brushes with respect to linear analogs. Denser and more compact cyclic brushes generate a steric barrier that surpasses the typical entropic shield by a linear brush. This phenomenon, translates into an improved resistance towards biological contamination from different protein mixtures. Moreover, the enhancement of steric stabilization coupled to the intrinsic absence of chain ends by cyclic brushes, produce surfaces displaying a super‐lubricating character when they are sheared against each other. All these topological effects pave the way for the application of cyclic brushes for surface functionalization, enabling the modulation of physico‐chemical properties that could be just marginally tuned by applying linear grafts.     

Diffraction engineering in arrays of photonic crystal waveguides

Light propagation in uniform arrays of photonic crystal waveguides is studied. We demonstrate that, in stark contrast to the case of conventional waveguide arrays, diffraction can be tailored both in magnitude and sign by varying only the spacing between adjacent waveguides. Diffraction management in ultracompact arrays of straight photonic crystal waveguides is demonstrated by solving Maxwell's equations through the time-domain finite-element method.     

An alternative for moduli stabilisation

The one-loop vacuum energy is explicitly computed for a class of perturbative string vacua where supersymmetry is spontaneously broken by a T-duality invariant asymmetric Scherk–Schwarz deformation. The low-lying spectrum is tachyon-free for any value of the compactification radii and thus no Hagedorn-like phase-transition takes place. Indeed, the induced effective potential is free of divergence, and has a global anti-de Sitter minimum where geometric moduli are naturally stabilised.     

Graphical operations on projective spaces

Motivated by the work of Crapo and Rota [6] on the lifting of a projective complex, we introduce a class of invariant operations associated to integral-weighted graphs, which we call graphical operations. Such operations generalize the sixth harmonic of a quadranguler set on a projective line. We determine the expansion of the graphical operations in terms of multi-linear bracket polynomials in a Grassmann-Cayley algebra. Reducibility and compositions of such invariant operations are also investigated with a number of examples.Supported by Courant Instructorship, New York University.